How to apply a check with a deduction to an invoice that was already paid

Hi, I need help on below, I have a customer who paid invoice 123 of $840 (2 transaction of $420 each) before, the fund was applied to undeposited fund acct and then deposit to the bank already. few days ago I received another check paying 2 invoices and a deduction of $420 on invoice # 123. The check was already deposited to the bank account when my boss gave me the check stub to offset the invoices. When I try to apply the payment, I notice I can't enter a negative amount when I apply the payment. My question is how can I apply that negative amount and have invoice 123 show a balance of $420 without adding another $420 to that invoice? I need invoice 123 to show a balance of $420, so I can send it to my customer for additional payment.

How to apply a check with a deduction to an invoice that was already paid

I appreciate you elaborating the complete details of your concern. I'm here to share some information about deducting payment on an invoice that was already deposited in QuickBooks Online (QBO).

Since you already deposited the payment for that specific invoice, you can unlink the other payment so it will only show a partial payment instead. That way, you'll no longer need to apply a negative amount on the invoice. Here's how:

1. Go to the Sales menu at the left pane, then select Customers.2. Choose the name of the customer, then click the invoice (invoice #123).3. On the right side of the invoice, click the payment made under Payment Status.4. Pick a date for that payment (there should be two payments made for $420 each), then uncheck the invoice under Description to remove the payment.5. Select Save and Close.6. On the You didn't select any invoices pop-up, click Save asa credit, then Yes.

Once done, you'll now see that invoice has now a balance of $420 and the Status is Partial. I also attached some sample screenshots for your visual guide.

For your reference, you can also check out this article for more information: Deposits FAQ.

That's it! Please let me know how it goes for you or if I can be of additional assistance. I'd be glad to answer should you have any questions. Wishing you and your business continued success.